View Abstract

REASSEMBLING 600+ MARINE TRANSCRIPTOMES: AUTOMATED PIPELINE DEVELOPMENT AND EVALUATION (E)

The Marine Microbial Eukaryotic Transcriptome Sequencing Project (MMETSP) facilitated the generation of 678 Illumina RNA sequence datasets from a wide diversity of organisms spanning more than 40 phyla of cultured microbial eukaryotes collected from a variety of marine environments. This is the largest publicly available set of RNA sequencing data from a diversity of eukaryotic taxa with a standardized library preparation. We developed an automated and modularized de novo transcriptome assembly pipeline for the MMETSP data set that is extensible to accommodate both future software updates and additional samples. With this large set of assemblies from a diversity of species, we were able to quantitatively evaluate the qualities of individual transcriptomes. Moreover, a meta-analysis across the dataset revealed lineage-specific transcriptome characteristics, such as predicted open reading frames, contig features, unique k-mers and evaluation scores. Ultimately, a better understanding of these assemblies and annotations will enhance our ability to accurately identify and characterize genes of ecological and biogeochemical significance.

Authors

Cohen, L. J., UC Davis, USA, ljcohen@ucdavis.edu

Alexander, H., UC Davis, USA, harriet.xander@gmail.com

Brown, C. T., UC Davis, USA, ctbrown@ucdavis.edu

Details

Oral presentation

Session #:016
Date: 03/03/2017
Time: 12:30
Location: 323 C

Presentation is given by student: Yes